Increasing competitiveness as well as levels of sustainability are some of the main challenges that the packaging sector is facing. The introduction of information and communication technologies provides new functionalities, such as traceability within logistic processes. In this context, RFID technologies can play a key role but can also pose hurdles, owing to increased cost, as well as to difficulties in relation with recycling and complying with product circularity. In this sense chipless RFID opens new possibilities, by avoiding the use of information coded chips, reducing costs in material and placement, as well by improving recyclability. In this work, a frequency based chipless RFID solution is presented, in which 2D geometrical patterns printed with conductive ink, resembling transmitive or reflective metasurfaces, are designed and integrated within paper-based substrates. An in-house reader system is implemented based on conventional Software Defined Radio platforms in the 0-6GHz and in the 0-12GHz range, in which received signal post-processing is performed to increase reader sensitivity, without the need of using Vector Network Analyzer equipment. Moreover, in order to reduce material waste, an automatic fault detection system based on artificial vision coupled to a robot arm is designed and tested. Different prototypes in paper substrates as well as in reference printed circuit boards have been fabricated and measured, showing good agreement. The proposed solution provides a feasible chipless RFID system with a portable low-cost reader which can be embedded in paper/cardboard materials in packaging applications.